Expanding use of whole genome sequencing pathogen analysis globally will improve trace back investigations during foodborne outbreaks, according to researchers.

A study published in the journal Eurosurveillance reports experiences of using whole genome sequencing (WGS) data to investigate outbreaks of Shiga toxin-producing E. coli (STEC) O157:H7 in England between 2013 and 2017.

The research scientists said more WGS use would ensure rapid implementation of interventions to protect public health, inform risk assessment, and help manage national and international foodborne outbreaks of the potentially deadly E. coli O157:H7.

In the 1990s and early 2000s, pulsed field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA,) respectively, were used reactively in outbreaks already identified by epidemiological links. Public Health England (PHE) implemented WGS as the molecular typing method for all isolates of E. coli O157:H7 in June 2015.

“Analysis of WGS data delivered an unprecedented level of strain discrimination when compared with MLVA. The robustness of the WGS method ensured confidence in the microbiological identification of linked cases, even when epidemiological links were obscured,” said researchers.

Forensic-level microbiological typing provided by WGS can generate a fine-tuned definition to identify outbreak patients.

There is often poor patient recall of food consumed before onset of symptoms in epidemiological investigations, particularly when the product is a side dish such as salad leaves or raw vegetables, or something such as herbs and spices in foods with multiple ingredients.

In a 2014 STEC outbreak associated with raw milk, four additional patients, identified by WGS, had consumed the milk but initially failed to recall an accurate food history or were unaware the milk was unpasteurized.

Analysis of the STEC O157:H7 dataset at PHE showed that by exploring the context of the deeper phylogenetic relationship between isolates, the source of infection could be linked to specific geographical regions of the United Kingdom.

Analysis of WGS data from a 2016 outbreak linked to contaminated mixed leaf salad revealed the outbreak strain belonged to an uncommon “clade” in the PHE database. The clade included a high proportion of patients reporting recent travel to Mediterranean countries, compared with other clades in the PHE database. imported red Batavia lettuce leaves were suspected as the vehicle of infection, although there was no microbiological evidence.

“As more countries implement standardized, open access WGS data for routine surveillance of STEC, cross border exchange of WGS data will have a major impact on the ability to investigate national and international outbreaks of foodborne disease,” said researchers.